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DDBJ with new system and face.

Sugawara H, Ogasawara O, Okubo K, Gojobori T, Tateno Y - Nucleic Acids Res. (2007)

Bottom Line: The released data contains the high-throughput cDNAs of cricket and high-quality draft genome of medaka among others.Our computer system has been upgraded since March 2007.Another new aspect is an efficient data retrieval tool that has recently been equipped and served at DDBJ.

View Article: PubMed Central - PubMed

Affiliation: Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan.

ABSTRACT
DDBJ (http://www.ddbj.nig.ac.jp) collected and released 1 880 115 entries or 1 134 086 245 bases in the period from July 2006 to June 2007. The released data contains the high-throughput cDNAs of cricket and high-quality draft genome of medaka among others. Our computer system has been upgraded since March 2007. Another new aspect is an efficient data retrieval tool that has recently been equipped and served at DDBJ. It is called All-round Retrieval for Sequence and Annotation, which enables the user to search for keywords also in the Feature/Qualifier of the International Nucleotide Sequence Database Collaboration (http://www.insdc.org/). We will also replace our home page with a more efficient one by the end of 2007.

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Example of keyword search by ARSA. Keywords used are ‘source’ (Feature), ‘chromosome’ (Qualifier belonging to ‘source’) and CDS (Feature). ‘Chromosome’ has a value attribute to which ‘Y’ is given for specifying chromosome Y.
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Figure 1: Example of keyword search by ARSA. Keywords used are ‘source’ (Feature), ‘chromosome’ (Qualifier belonging to ‘source’) and CDS (Feature). ‘Chromosome’ has a value attribute to which ‘Y’ is given for specifying chromosome Y.

Mentions: ARSA covers 23 databases including DDBJ, UniProt, PFAM, PDB and LENZYME. A special feature of ARSA is that it can also incorporate the terms defined by the Feature/Qualifier of INSDC. While this feature is very helpful for us to annotate the submitted data, it enables our user to perform data retrieval by using terms in the Feature/Qualifier. For example, you can search for CDSs (protein coding sequences) located on human Y chromosome, as shown in Figure 1. In the figure, the query formula is given on the top, and a part of the hit entries is given below with the accession numbers. By clicking one of the numbers you can see its contents. HUM in the last column stands for the human division. You can download the search result in Flat File, FASTA or XML, and also choose the items in the search results to be displayed on the computer screen and directly download them in tab-limited format. We also provide you with WebAPI (http://xml.nig.ac.jp/>http://xml.nig.ac.jp/) (12) so that you can customize ARSA by writing a program in Perl or JAVA. We will soon include KEGG (http://www.genome.ad.jp/kegg/) in ARSA and make the 24 databases simultaneously retrievable for common keywords.Figure 1.


DDBJ with new system and face.

Sugawara H, Ogasawara O, Okubo K, Gojobori T, Tateno Y - Nucleic Acids Res. (2007)

Example of keyword search by ARSA. Keywords used are ‘source’ (Feature), ‘chromosome’ (Qualifier belonging to ‘source’) and CDS (Feature). ‘Chromosome’ has a value attribute to which ‘Y’ is given for specifying chromosome Y.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238829&req=5

Figure 1: Example of keyword search by ARSA. Keywords used are ‘source’ (Feature), ‘chromosome’ (Qualifier belonging to ‘source’) and CDS (Feature). ‘Chromosome’ has a value attribute to which ‘Y’ is given for specifying chromosome Y.
Mentions: ARSA covers 23 databases including DDBJ, UniProt, PFAM, PDB and LENZYME. A special feature of ARSA is that it can also incorporate the terms defined by the Feature/Qualifier of INSDC. While this feature is very helpful for us to annotate the submitted data, it enables our user to perform data retrieval by using terms in the Feature/Qualifier. For example, you can search for CDSs (protein coding sequences) located on human Y chromosome, as shown in Figure 1. In the figure, the query formula is given on the top, and a part of the hit entries is given below with the accession numbers. By clicking one of the numbers you can see its contents. HUM in the last column stands for the human division. You can download the search result in Flat File, FASTA or XML, and also choose the items in the search results to be displayed on the computer screen and directly download them in tab-limited format. We also provide you with WebAPI (http://xml.nig.ac.jp/>http://xml.nig.ac.jp/) (12) so that you can customize ARSA by writing a program in Perl or JAVA. We will soon include KEGG (http://www.genome.ad.jp/kegg/) in ARSA and make the 24 databases simultaneously retrievable for common keywords.Figure 1.

Bottom Line: The released data contains the high-throughput cDNAs of cricket and high-quality draft genome of medaka among others.Our computer system has been upgraded since March 2007.Another new aspect is an efficient data retrieval tool that has recently been equipped and served at DDBJ.

View Article: PubMed Central - PubMed

Affiliation: Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan.

ABSTRACT
DDBJ (http://www.ddbj.nig.ac.jp) collected and released 1 880 115 entries or 1 134 086 245 bases in the period from July 2006 to June 2007. The released data contains the high-throughput cDNAs of cricket and high-quality draft genome of medaka among others. Our computer system has been upgraded since March 2007. Another new aspect is an efficient data retrieval tool that has recently been equipped and served at DDBJ. It is called All-round Retrieval for Sequence and Annotation, which enables the user to search for keywords also in the Feature/Qualifier of the International Nucleotide Sequence Database Collaboration (http://www.insdc.org/). We will also replace our home page with a more efficient one by the end of 2007.

Show MeSH